DNA methylation signatures of early life adversity are exposure-dependent (Anderson et al. 2023, BioRxiv)
This Github repository contains all of the code for intermediate processing and visualization of our major results related to identified socioenvironmental links to gene regulation. This includes intersecting multiple lines of genomic data, performing enrichment tests, building a binomial elastic-net classifier, and more. The repository and associated README can be found here: https://github.com/janderson94/Anderson_et_al_socioecological_methylation_predictors.
Epigenetic aging predictions and socio-environmental predictors (Anderson et al. 2021, eLife)
This Github repository includes parallel, leave-one-out, elastic net model building that can be easily modified for a variety of purposes. We also include related scripts to recreate results relating socio-environmental predictors (e.g. social status) and relative epigenetic age. The repository and associated README can be found here: github.com/janderson94/BaboonEpigeneticAging
Social environmental predictors of immune gene regulation (Anderson et al. 2022, Phil Trans)
This work explores how variation in social factors, namely social status and social integration, are reflected in differences in immune gene expression. This Github repository houses all of the major analyses relating to filtering gene expression data, removing known technical effects, and modeling for an effect of social factors on the resulting gene expression levels. We also provide code using for Gene Set Enrichment Analyses, as well as leave-one-out elastic net predictions of dominance rank included in our preprint. The repository and associated README can be found here: github.com/janderson94/Anderson_et_al_distinct_social_signatures.
This Github repository contains all of the code for intermediate processing and visualization of our major results related to identified socioenvironmental links to gene regulation. This includes intersecting multiple lines of genomic data, performing enrichment tests, building a binomial elastic-net classifier, and more. The repository and associated README can be found here: https://github.com/janderson94/Anderson_et_al_socioecological_methylation_predictors.
Epigenetic aging predictions and socio-environmental predictors (Anderson et al. 2021, eLife)
This Github repository includes parallel, leave-one-out, elastic net model building that can be easily modified for a variety of purposes. We also include related scripts to recreate results relating socio-environmental predictors (e.g. social status) and relative epigenetic age. The repository and associated README can be found here: github.com/janderson94/BaboonEpigeneticAging
Social environmental predictors of immune gene regulation (Anderson et al. 2022, Phil Trans)
This work explores how variation in social factors, namely social status and social integration, are reflected in differences in immune gene expression. This Github repository houses all of the major analyses relating to filtering gene expression data, removing known technical effects, and modeling for an effect of social factors on the resulting gene expression levels. We also provide code using for Gene Set Enrichment Analyses, as well as leave-one-out elastic net predictions of dominance rank included in our preprint. The repository and associated README can be found here: github.com/janderson94/Anderson_et_al_distinct_social_signatures.